scholarly journals Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3266 ◽  
Author(s):  
Emma C. Wallace ◽  
Lina M. Quesada-Ocampo
Keyword(s):  
Downy Mildew ◽  
Draft Genome ◽  
Model Organism ◽  
Genomic Analysis ◽  
Population Level ◽  
Comparative Genomic ◽  
Pathogen Population ◽  
Pseudoperonospora Humuli ◽  
Hyaloperonospora Arabidopsidis

Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.

Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections

2020 ◽  
Vol 76 (1) ◽  
pp. 91-100
Author(s):  
Jorge Arca-Suárez ◽  
Cristina Lasarte-Monterrubio ◽  
Bruno-Kotska Rodiño-Janeiro ◽  
Gabriel Cabot ◽  
Juan Carlos Vázquez-Ucha ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Molecular Mechanisms ◽  
Genomic Analysis ◽  
Resistance Mechanisms ◽  
Comparative Genomic ◽  
Development Of Resistance ◽  
Structural Impact ◽  
Genetic Context

Abstract Background The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning. Objectives Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections. Methods Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes. Results The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold. Conclusions Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

Comparative genomic analysis of a mammalian β-defensin gene cluster

2007 ◽  
Vol 30 (3) ◽  
pp. 213-222 ◽  
Author(s):  
Yashwanth Radhakrishnan ◽  
Mario A. Fares ◽  
Frank S. French ◽  
Susan H. Hall
Keyword(s):  
Positive Selection ◽  
Gene Cluster ◽  
Genomic Analysis ◽  
Urogenital Tract ◽  
Comparative Genomic ◽  
Evolutionary Analysis ◽  
Defensin Gene ◽  
Duplication Events ◽  
Molecular Evolutionary Analysis

Comparative genomic analyses have yielded valuable insights into conserved and divergent aspects of gene function, regulation, and evolution. Herein, we describe the characterization of a mouse β-defensin gene cluster locus on chromosome 2F6. In addition, we present the evolutionary analysis of this cluster and its human, rhesus, and rat orthologs. Expression analysis in mouse revealed the occurrence of defensin cluster transcripts in multiple tissues, with the highest abundance in the urogenital tract. Molecular evolutionary analysis suggests that this cluster originated by a series of duplication events, and by positive selection occurring even after the rodent-primate split. In addition, the constraints analysis showed higher positive selection in rodents than in primates, especially distal to the six-cysteine array. Positive selection in the evolution of these defensins may relate not only to the evolving enhancement of ancestral host defense but also to functional innovations in reproduction. The multiplicity of defensins and their preferential overexpression in the urogenital tract indicate that defensins function in the protection and maintenance of fertility.

scholarly journals Comparative Genomic Analysis and Phenotypic Characterization of Bronchoscope-Associated Klebsiella aerogenes

2021 ◽  
Vol 70 (3) ◽  
pp. 409-412
Author(s):  
FANG HUANG ◽  
SHUANG LI ◽  
LAN LOU ◽  
JUNJUN MO ◽  
HAO XU
Keyword(s):  
Antimicrobial Agents ◽  
Genomic Analysis ◽  
Phenotypic Characterization ◽  
Comparative Genomic ◽  
Klebsiella Aerogenes ◽  
Clinical Procedures ◽  
First Time ◽  
Sequence Types ◽  
Level Resistance

Bronchoscopes have been linked to outbreaks of nosocomial infections. The phenotypic and genomic profiles of bronchoscope-associated Klebsiella aerogenes isolates are largely unknown. In this work, a total of 358 isolates and 13 isolates were recovered from samples after clinical procedures and samples after decontamination procedures, respectively, over the five months. Antimicrobial susceptibility testing found seven K. aerogenes isolates exhibiting a low-level resistance to antimicrobial agents. Among seven K. aerogenes isolates, we found five sequence types (STs) clustered into three main clades. Collectively, this study described for the first time the phenotypic and genomic characteristics of bronchoscope-associated K. aerogenes.

scholarly journals Characterization of a blaNDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin

2021 ◽  
Vol 11 ◽  
Author(s):  
Ziyi Liu ◽  
Ruifei Chen ◽  
Poshi Xu ◽  
Zhiqiang Wang ◽  
Ruichao Li
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Genetic Composition ◽  
Carbapenem Resistant ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
History Of ◽  
Core Genes

The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The blaNDM-1 gene was located on a ΔISAba125-blaNDM-1-bleMBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.

scholarly journals Draft Genome Sequence of Listeria monocytogenes CIIMS-NV-3, a Strain Isolated from Vaginal Discharge of a Woman from Central India

2019 ◽  
Vol 8 (6) ◽  
Author(s):  
Pooja M. Kishnani ◽  
Nitin V. Kurkure ◽  
Sukhadeo B. Barbuddhe ◽  
Swapnil P. Doijad ◽  
Trinad Chakraborty ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Genome Sequence ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Central India ◽  
Vaginal Swab ◽  
Comparative Genomic Analysis ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type

We present here the draft genome sequence of Listeria monocytogenes CIIMS-NV-3, a serovar 4b strain isolated from the vaginal swab of a female patient from central India. The availability of this genome may provide useful information on virulence characteristics for comparative genomic analysis.

scholarly journals Draft Genome Sequence of Vibrio vulnificus 86573B, a Bacterium Isolated from Diseased Tilapia in Taiwan

2018 ◽  
Vol 7 (1) ◽  
Author(s):  
Shu-Ting Cho ◽  
Yi-Ming Tsai ◽  
Chun-Yao Chen ◽  
Chih-Horng Kuo
Keyword(s):  
Genome Sequence ◽  
Vibrio Vulnificus ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Draft Genome Sequence ◽  
Comparative Genomic ◽  
Content Type

Vibrio vulnificus 86573B is a biotype 1 strain isolated from a moribund tilapia collected in Kaohsiung, Taiwan, during an outbreak early in 1997. Here, we report the draft genome sequence of this bacterium to facilitate the investigation of its biology and future comparative genomic analysis.

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